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synthego-open / ice

Synthego ICE - Inference of CRISPR Editing software
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AttributeError: 'MultipleSeqAlignment' object has no attribute 'format' #35

Open kiavash17 opened 2 years ago

kiavash17 commented 2 years ago

Hi Thanks for sharing this tool. After installation when running the example I get the following error:

$ synthego_ice --control ./ice/tests/test_data/good_example_control.ab1 --edited ./ice/tests/test_data/good_example_edited.ab1 --target AACCAGTTGCAGGCGCCCCA --out results/testing --verbose

Synthego ICE (https://synthego.com)
Version: 1.1.1-alpha1
Base dir: /rhampseq/kkiaee/ice/ice/results
Exception Caught!
Traceback (most recent call last):
  File "/home/ccadmin/anaconda3/envs/ice_env/lib/python3.8/site-packages/ice/analysis.py", line 82, in single_sanger_analysis
    sa.analyze_sample()
  File "/home/ccadmin/anaconda3/envs/ice_env/lib/python3.8/site-packages/ice/classes/sanger_analysis.py", line 799, in analyze_sample
    alignment.align_all()
  File "/home/ccadmin/anaconda3/envs/ice_env/lib/python3.8/site-packages/ice/classes/pair_alignment.py", line 94, in align_all
    self.all_aligned_clustal = self.align_list_to_clustal(aln, "control", "edited")
  File "/home/ccadmin/anaconda3/envs/ice_env/lib/python3.8/site-packages/ice/classes/pair_alignment.py", line 80, in align_list_to_clustal
    alignment_txt = aln_objs[0].format("clustal").split('\n', 2)[2]
AttributeError: 'MultipleSeqAlignment' object has no attribute 'format'

I'd appreciate your help in troubleshooting this.

zhoubin1999 commented 2 years ago

change format to __format__

innoxHenan commented 2 years ago

Hi, I've encoutered the same error message. I tried change 'format' to 'format' for analysis.py, sanger_analysis.py and pair_alignment.py, but it did not work. How did you solve it?

thuanguyen commented 2 years ago

I have a same problem. please help.

thuanguyen commented 2 years ago

change format to __format__

I do not understand what do you mean by change format to __format__. In which file I need to change it?

asyafiqe commented 1 year ago

change format to __format__

I do not understand what do you mean by change format to __format__. In which file I need to change it?

pair_alignment.py, line 80 alignment_txt = aln_objs[0].__format__("clustal").split('\n', 2)[2]

einsidhe commented 1 year ago

Hi folks. Actually changing 'format' to 'format' doesn't help. Have anybody found the solution?

sshen8 commented 1 year ago

I was able to get around this issue with pip install biopython==1.78 MultipleSeqAlignment.format was deprecated and removed after biopython v1.78 (docs)